Opened in amphtml repo as well:

Using ampproject/toolbox-optimizer with Amp Stories:
The toolbox-optimizer Extract and move CSS keyframe animations to the bottom of the page.
Now has sibling <style amp-keyframes>
But with atual rules of validate: Tag ‘amp-story’ is not allowed to have any sibling tags (‘body’ should only have 1 child).

Add <style amp-keyframes> as a possible sibling to validade?